Methanobacterium thermoautotrophicum

Genes

DNA-dependent RNA polymerase, subunit A' (ref|NP_276181.1)
DNA directed RNA polymerase II polypeptide A? (ref|NP_000928.1|)

From the brief descriptions of both Protein A (DNA-dependent RNA polymerase, subunit A' ) and Protein B (DNA directed RNA polymerase II polypeptide A), it's obvious that both proteins perform functions in translation/transcription. They are both encoded by genes involved in transcription and RNA processing. More specifically about protein B, genes in B encode the largest subunit of RNA polymerase II. This subunit, in combination with several other polymerase subunits, forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA (source: LocusLink)

Alignment


	Score =  663 bits (1711), Expect = 0.0
Identities = 366/907 (40%), Positives = 541/907 (59%), Gaps = 66/907 (7%)

Query: 5   LKKISQINFGLMSPEDIRKMSVTQ--IVTPDTYDEDGYPIENGLMDPRLGVIDPSLRCRT 62
           L+ I ++ FG++SP+++++MSVT+  I  P+T  E G P   GLMDPR GVI+ + RC+T
Sbjct: 15  LRTIKRVQFGVLSPDELKRMSVTEGGIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQT 73

Query: 63  CGAKGGECPGHFGSINLARPVIHVGFADTIHKILRSTCRKCGRVLLTETEIEEYRQRILD 122
           C     ECPGHFG I LA+PV HVGF     K+LR  C  C ++L     ++    +I D
Sbjct: 74  CAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLL-----VDSNNPKIKD 128

Query: 123 AMEKEESLTPI-IKEIYAEAR-RDKCPHCEEEQEEIKLDKPVSIVEGDYKLT-------- 172
            + K +      +  +Y   + ++ C   EE   +  +++P    EGD  LT        
Sbjct: 129 ILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQP----EGDEDLTKEKGHGGC 184

Query: 173 ---------------------------------PSEVRERLERISDDDALILGVNPEVAR 199
                                            P  V E  +RISD++  +LG+ P  AR
Sbjct: 185 GRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYAR 244

Query: 200 PEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDILRINQRLKENMEAGAPQLIVE 259
           PEWM++TVLPVPP++VRP++ ++   R++DDLTHKL DI++IN +L+ N + GA   ++ 
Sbjct: 245 PEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIA 304

Query: 260 DLWELLQYHVTTYFDNEASGVPPARHRSGRPLKTLAQRLKGKEGRFRSNLSGKRVNFSAR 319
           +  +LLQ+HV T  DNE  G+P A  +SGRPLK+L QRLKGKEGR R NL GKRV+FSAR
Sbjct: 305 EDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSAR 364

Query: 320 TVISPDPNISINEVGVPEIIAREVTVPVYVTEWNIDRMREYIENGPDVHPGANYVIRPDG 379
           TVI+PDPN+SI++VGVP  IA  +T    VT +NIDR++E +  G   +PGA Y+IR +G
Sbjct: 365 TVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNG 424

Query: 380 RKIRIYNETKEVVLENLKPGYIVERHLKDGDIVLFNRQPSLHRMSMMAHQVRVLPYKTFR 439
            +I +    K   L +L+ GY VERH+ DGDIV+FNRQP+LH+MSMM H+VR+LP+ TFR
Sbjct: 425 DRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 483

Query: 440 LNLCVCPPYNADFDGDEMNMHVFQTEESRAEAKTLMRVQEHILSPRFGGPIIGGIHDHIS 499
           LNL V  PYNADFDGDEMN+H+ Q+ E+RAE + L  V   I++P+   P++G + D ++
Sbjct: 484 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLT 543

Query: 500 GAYLLTRKSAVFSEEKVFQILK-------KAGLPLPDSRGRDWTGKEIFSMVLPDDLNMV 552
                T++       +V  +L        K   P        WTGK+IFS+++P  +N +
Sbjct: 544 AVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCI 603

Query: 553 YRAEVCRKCEEC--LEMECENDAYVVIENGQLISGVIDEKAYGAFAGKILDHIVKEYGTD 610
                    E+    +     D  VV+ENG+LI G++ +K+ G  AG ++     E G D
Sbjct: 604 RTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHD 663

Query: 611 AAREFLDSATKLAIAGIMHAGFTTSTNDEEIPEEARERIEAHLRNAEARVDQLIEAYENG 670
             R F  +   +    ++  G T    D     +  + I+  ++ A+  V ++IE   N 
Sbjct: 664 ITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNN 723

Query: 671 ELEPLPGRSLEETLEMKIMQVLGEARDKSGEIAESYFDMDENHAVIMALTGARGSMLNLT 730
           ELEP PG +L +T E ++ ++L +ARDK+G  A+     + N+   M ++GA+GS +N++
Sbjct: 724 ELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLS-EYNNFKSMVVSGAKGSKINIS 782

Query: 731 QITACVGQQSVRGGRISRGYDNRTLPHFKKGELGAKSRGFVHSSYKEGLDPIEFFFHAMG 790
           Q+ A VGQQ+V G RI  G+ +RTLPHF K + G +SRGFV +SY  GL P EFFFHAMG
Sbjct: 783 QVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMG 842

Query: 791 GREGLVDTAIRTAQSGYMQRRLVNALQDLTVDENGRVVDNRGVIIQNRFGEDGVDPAKSD 850
           GREGL+DTA++TA++GY+QRRL+ +++ + V  +  V ++   ++Q R+GEDG+     +
Sbjct: 843 GREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVE 902

Query: 851 YGKIVDL 857
           +  +  L
Sbjct: 903 FQNLATL 909